Objective: Build a simple web service which parses a standalone GFF3 file containing translated small ORFs reported in Hsu et al. (PNAS 2016), and returns this data in JBrowse compatible JSON format.
The adapter utilizes gffutils to process the input GFF3 file, creating an intermediary sqlite database for fast data retrieval.
Reference:
Hsu, Polly Yingshan, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler, and Philip N. Benfey. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings of the National Academy of Sciences 113, no. 45 (2016): E7126-E7135. doi:10.1073/pnas.1614788113
Requirements:
- Enable the following plugin in JBrowse within
tracks.conf:- Araport REST with bindings to ADAMA
[plugins]
Araport.location = ./plugins/Araport
- This adapter relies on storing the GFF3 file corresponding to the annotated small ORFs in the
data/sub-directory.
data/pnas.1614788113_SupplementalDS1.gff3
-
Ensure that the small_orfs_to_jbrowse adapter is registered and accessible via ADAMA. See metadata.yml for adapter configuration (list of dependency modules and REST endpoints described using swagger.io spec).
-
Set up the following track configuration in JBrowse within
trackList.json:
{
"style" : {
"color" : "plum"
},
"key" : "Translated small ORFs (Hsu et al. 2016)",
"storeClass" : "Araport/Store/SeqFeature/REST",
"baseUrl" : "%(api_url)s",
"type" : "JBrowse/View/Track/CanvasFeatures",
"category" : "Community Data / Genomic Elements",
"metadata" : {
"Description" : "Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis",
"Source" : "Hsu et al. 2016 (PNAS)",
"URL" : "http://www.pnas.org/content/113/45/E7126.full"
},
"glyph" : "JBrowse/View/FeatureGlyph/Gene",
"label" : "translated_small_ORFs_Hsu_et_al"
}